Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000638.1 Hibiscus syriacus cultivar Beakdansim tig00001235_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 74803
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:3558 original size:4 final size:4
Alignment explanation
Indices: 3549--3579 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3539 ATCTGGAATC
3549 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
3580 CTTCGTGCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:4874 original size:45 final size:45
Alignment explanation
Indices: 4779--4882 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
4769 TGCACTCCTT
* *
4779 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
4824 ATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
4868 AGTGCATCGATGCAC
1 A-TGCATCGATGCAC
4883 TACTAATGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 2 0.04
45 43 0.84
46 6 0.12
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (45 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:11056 original size:15 final size:15
Alignment explanation
Indices: 11036--11068 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
11026 CGTAGGACCC
*
11036 CTACATCCTGAAGGA
1 CTACATCCCGAAGGA
11051 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
11066 CTA
1 CTA
11069 TTATACCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:11676 original size:64 final size:63
Alignment explanation
Indices: 11556--11739 Score: 235
Period size: 64 Copynumber: 2.9 Consensus size: 63
11546 TAATGAAGGT
* * ** * * **
11556 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCAATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTATTATTAATGGG
* **
11620 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTT-ATTATTAATGGG
*
11684 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTT-TTATT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATT
11740 TTAAAAGAGT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
62 5 0.05
63 2 0.02
64 98 0.93
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:11753 original size:64 final size:64
Alignment explanation
Indices: 11556--11773 Score: 208
Period size: 64 Copynumber: 3.4 Consensus size: 64
11546 TAATGAAGGT
* * ** ** * * *** *
11556 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCAATGTATT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
11620 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
11684 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGAG
**
11747 AGTGCATCGATGCACTACCAATGCATC
1 A-TGCATCGATGCACTACTTATGCATC
11774 AATACATCTT
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.03
64 122 0.92
65 6 0.05
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:12736 original size:20 final size:20
Alignment explanation
Indices: 12711--12764 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
12701 AGTGTTATTT
12711 GTGTATCGATACACTGAGGA
1 GTGTATCGATACACTGAGGA
*
12731 GTGTATC-AGTACATTGAGGA
1 GTGTATCGA-TACACTGAGGA
12751 GTGTATCGATACAC
1 GTGTATCGATACAC
12765 CCAAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (20 bp):
GTGTATCGATACACTGAGGA
Found at i:12791 original size:75 final size:75
Alignment explanation
Indices: 12657--12812 Score: 231
Period size: 75 Copynumber: 2.1 Consensus size: 75
12647 TGTATGAATA
** * *
12657 TGTATCAGTACACTGAAGAGTGTATCGATACACCCAAAACATCGAGTGTTATTTGTGTATCGATA
1 TGTATCAGTACACTGAAGAGTGTATCGATACACCCAAAACATCGAGTGCAAATTATGTATCGATA
*
12722 CACTGAGGAG
66 CACTAAGGAG
* * * *
12732 TGTATCAGTACATTGAGGAGTGTATCGATACACCCAAAACATTGAGTGCAAATTATGTATCGGTA
1 TGTATCAGTACACTGAAGAGTGTATCGATACACCCAAAACATCGAGTGCAAATTATGTATCGATA
12797 CACTAAGGAG
66 CACTAAGGAG
12807 TGTATC
1 TGTATC
12813 GATACTAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (75 bp):
TGTATCAGTACACTGAAGAGTGTATCGATACACCCAAAACATCGAGTGCAAATTATGTATCGATA
CACTAAGGAG
Found at i:18409 original size:31 final size:31
Alignment explanation
Indices: 18374--18433 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
18364 GTGTTCTATG
18374 CGAGCTGTGACGAGAGGATAAAGCTTTGCTA
1 CGAGCTGTGACGAGAGGATAAAGCTTTGCTA
** *
18405 CGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 CGAGCTGTGACGAGAGGATAAAGCTTTGC
18434 ATGCGCCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.37, T:0.23
Consensus pattern (31 bp):
CGAGCTGTGACGAGAGGATAAAGCTTTGCTA
Found at i:18488 original size:21 final size:22
Alignment explanation
Indices: 18437--18488 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
18427 GCTTTGCATG
*
18437 CGCCATTCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
18459 CGCCATGCACGTCGGAAGAGGT
1 CGCCATGCACGTCGGAAGAGGT
18481 CG-CATGCA
1 CGCCATGCA
18489 TGCAGCGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.23, C:0.29, G:0.33, T:0.15
Consensus pattern (22 bp):
CGCCATGCACGTCGGAAGAGGT
Found at i:18573 original size:29 final size:29
Alignment explanation
Indices: 18534--18621 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
18524 AGGGCGCAGG
* * *
18534 ACAAGGACGCCCAGCGCGCATGGCGACCT
1 ACAAGGTCGCCCGGAGCGCATGGCGACCT
* * * * *
18563 ACCATGTCGCCTGGTGTGCATGGCGACCT
1 ACAAGGTCGCCCGGAGCGCATGGCGACCT
*
18592 ACAAGGTCGCCCGGAGGGCATGGCGACCT
1 ACAAGGTCGCCCGGAGCGCATGGCGACCT
18621 A
1 A
18622 TGCTGGGAAG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.14
Consensus pattern (29 bp):
ACAAGGTCGCCCGGAGCGCATGGCGACCT
Found at i:21242 original size:21 final size:21
Alignment explanation
Indices: 21218--21259 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21208 GAAAATAGAT
21218 TAAAAAA-ACAGAATATACAAC
1 TAAAAAAGACAGAATA-ACAAC
*
21239 TAAAAAAGACATAATAACAAC
1 TAAAAAAGACAGAATAACAAC
21260 AATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.67, C:0.14, G:0.05, T:0.14
Consensus pattern (21 bp):
TAAAAAAGACAGAATAACAAC
Found at i:32842 original size:18 final size:18
Alignment explanation
Indices: 32819--32859 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
32809 AGGCATTTGA
32819 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTCGTGCTTGT
*
32837 TCCTCTGCTCGTTCTTGT
1 TCCTCTGCTCGTGCTTGT
32855 TCCTC
1 TCCTC
32860 GTGTTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.00, C:0.34, G:0.20, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTCGTGCTTGT
Found at i:34444 original size:22 final size:22
Alignment explanation
Indices: 34412--34472 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
34402 CCAGAACCCC
34412 AGGGGGTATCGATTCCCCTACA
1 AGGGGGTATCGATTCCCCTACA
* * * *
34434 GGGGGGAATCGGTTCCCCTTCA
1 AGGGGGTATCGATTCCCCTACA
34456 AGGGGGTATCGATTCCC
1 AGGGGGTATCGATTCCC
34473 TCTGTACTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (22 bp):
AGGGGGTATCGATTCCCCTACA
Found at i:45010 original size:20 final size:20
Alignment explanation
Indices: 44985--45193 Score: 158
Period size: 20 Copynumber: 10.2 Consensus size: 20
44975 AATGACAAAC
* *
44985 AAAATCGTAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
45005 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
45025 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
45045 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
45066 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
45087 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
45108 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
45129 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
45151 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
* *
45169 AAAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTAAG
45189 AAAAT
1 AAAAT
45194 GAGTAAATTC
Statistics
Matches: 152, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
18 4 0.03
20 105 0.69
21 13 0.09
22 30 0.20
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:45093 original size:42 final size:42
Alignment explanation
Indices: 45042--45184 Score: 227
Period size: 42 Copynumber: 3.5 Consensus size: 42
45032 CAACGGTCAA
*
45042 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* *
45084 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
45126 CAGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
45166 AAGAAAATCGCAATGCGAT
1 AAGAAAATCGCAACGCGAT
45185 TCAGAAAATG
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
40 37 0.41
42 54 0.59
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
Found at i:45300 original size:6 final size:6
Alignment explanation
Indices: 45289--45319 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
45279 GACATGTATT
45289 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
45320 GACGGCGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:45852 original size:6 final size:5
Alignment explanation
Indices: 45803--45848 Score: 65
Period size: 5 Copynumber: 8.6 Consensus size: 5
45793 CCGTCTCGTC
45803 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
45849 TGGTAATACG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 23 0.57
6 17 0.43
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:46025 original size:22 final size:20
Alignment explanation
Indices: 45955--46115 Score: 168
Period size: 20 Copynumber: 7.8 Consensus size: 20
45945 CTCATTTTCT
* *
45955 GAATCGCATTGCGGTTCTTG
1 GAATCGCGTTGCGATTCTTG
45975 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
45996 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
46015 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
46037 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-G
*
46059 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
46079 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
46099 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
46116 CTTCTTTTCA
Statistics
Matches: 127, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.04
20 60 0.47
21 7 0.06
22 55 0.43
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:46035 original size:62 final size:62
Alignment explanation
Indices: 45948--46177 Score: 260
Period size: 62 Copynumber: 3.8 Consensus size: 62
45938 GAATTTACTC
* *
45948 ATTTTCTG-AATCGCATTGCGGTTCTTGG-A-ATCGCGTTGCGATTTTCTTAATCGCGTTGCG
1 ATTTTC-GAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCG
* *
46008 ATTCTTGGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATT-TTCGAA-ATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCG
* * *
46072 ATTTTCTG-AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATCTTCTT-TTCAACGTTGCG
1 ATTTTC-GAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATC-GCGTTGCG
* * * *
46134 GTTTTCTAAATCGCGTTGCGGTT-TT-G-ATATCGCGTTGCGATTTT
1 ATTTTCGAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTT
46178 GTTGGTCATT
Statistics
Matches: 148, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
59 16 0.11
60 5 0.03
61 7 0.05
62 82 0.55
63 4 0.03
64 34 0.23
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (62 bp):
ATTTTCGAAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCG
Found at i:46150 original size:20 final size:20
Alignment explanation
Indices: 45976--46177 Score: 174
Period size: 20 Copynumber: 9.8 Consensus size: 20
45966 CGGTTCTTGG
*
45976 AATCGCGTTGCGATTTTCTT
1 AATCGCGTTGCGATTTTCTA
**
45996 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
**
46017 AGATCGCGTTGCGATTCTTGGA
1 A-ATCGCGTTGCGATT-TTCTA
*
46039 AGATCGCGTTGCGATTTTCTG
1 A-ATCGCGTTGCGATTTTCTA
*
46060 AATCGCGTTGCGATTTTCTG
1 AATCGCGTTGCGATTTTCTA
**
46080 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTA
*
46101 AGATCGCGTTGCGATCTTCT-
1 A-ATCGCGTTGCGATTTTCTA
** * *
46121 TTTCAACGTTGCGGTTTTCTA
1 AATC-GCGTTGCGATTTTCTA
* *
46142 AATCGCGTTGCGGTTTT-GA
1 AATCGCGTTGCGATTTTCTA
*
46161 TATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
46178 GTTGGTCATT
Statistics
Matches: 153, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
19 18 0.12
20 73 0.48
21 13 0.08
22 49 0.32
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCTA
Found at i:48042 original size:20 final size:19
Alignment explanation
Indices: 48006--48049 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
47996 CACTTTTATC
*
48006 ACTCCAAATTTTCTCAAAT
1 ACTCTAAATTTTCTCAAAT
*
48025 TCTCTAAATTTCTCTCAAAT
1 ACTCTAAATTT-TCTCAAAT
48045 ACTCT
1 ACTCT
48050 CTTTTAAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (19 bp):
ACTCTAAATTTTCTCAAAT
Found at i:52896 original size:25 final size:23
Alignment explanation
Indices: 52867--52940 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 23
52857 TATATATATA
52867 TATATATAATATTTTTTATATTAAT
1 TATATAT-ATA-TTTTTATATTAAT
52892 TATATATATAATATTTTATA-T-AT
1 TATATATAT-AT-TTTTATATTAAT
52915 T-T-TATATA-TTTTATATTAAT
1 TATATATATATTTTTATATTAAT
52935 TATATA
1 TATATA
52941 AAAAATATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
18 7 0.16
19 1 0.02
20 4 0.09
21 6 0.14
22 3 0.07
23 3 0.07
24 4 0.09
25 15 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATATATATTTTTATATTAAT
Found at i:52897 original size:27 final size:25
Alignment explanation
Indices: 52855--52923 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 25
52845 ACCCCGATTA
*
52855 TATATATATATATATATATAATATTT
1 TATATAT-TTTATATATATAATATTT
*
52881 TTTATATTAATTATATATATAATATTT
1 TATATATT--TTATATATATAATATTT
52908 TATATATTTTATATAT
1 TATATATTTTATATAT
52924 TTTATATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 9 0.24
26 6 0.16
27 23 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATATTTTATATATATAATATTT
Found at i:52914 original size:43 final size:43
Alignment explanation
Indices: 52853--52951 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 43
52843 CCACCCCGAT
* *
52853 TATATAT-ATA-TATATATATATAATATTTTTTATATTAATTA
1 TATATATAATATTTTATATATATAATATATTTTATATTAATTA
* *
52894 TATATATAATATTTTATATATTTTATATATTTTATATTAATTA
1 TATATATAATATTTTATATATATAATATATTTTATATTAATTA
* *
52937 TATAAAAAATATTTT
1 TATATATAATATTTT
52952 CGGGTTCGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 7 0.14
42 3 0.06
43 40 0.80
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (43 bp):
TATATATAATATTTTATATATATAATATATTTTATATTAATTA
Found at i:52927 original size:9 final size:9
Alignment explanation
Indices: 52852--52930 Score: 65
Period size: 9 Copynumber: 8.7 Consensus size: 9
52842 CCCACCCCGA
52852 TTATATA-T
1 TTATATATT
*
52860 ATATATATAT
1 TTATATAT-T
*
52870 ATATAATATT
1 TTAT-ATATT
*
52880 TTTTATATT
1 TTATATATT
52889 AATTATATA-T
1 --TTATATATT
*
52899 ATA-ATATT
1 TTATATATT
52907 TTATATATT
1 TTATATATT
52916 TTATATATT
1 TTATATATT
52925 TTATAT
1 TTATAT
52931 TAATTATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
7 3 0.05
8 11 0.19
9 25 0.43
10 9 0.16
11 10 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTATATATT
Found at i:52940 original size:2 final size:2
Alignment explanation
Indices: 52853--52923 Score: 50
Period size: 2 Copynumber: 39.5 Consensus size: 2
52843 CCACCCCGAT
* *
52853 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TT TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
52891 T- TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52924 TTTATATTAA
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
1 8 0.14
2 50 0.86
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:53287 original size:31 final size:30
Alignment explanation
Indices: 53226--53290 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
53216 TAAGAGAAAA
* *
53226 TAGTCCTAACGTTATCGATTCGTTCAATTT
1 TAGTCCTAACGTTATCGATCCATTCAATTT
* **
53256 TAGTCCCTAATGTTATCGATCCATTTGATTT
1 TAGT-CCTAACGTTATCGATCCATTCAATTT
53287 TAGT
1 TAGT
53291 TTCTCATCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (30 bp):
TAGTCCTAACGTTATCGATCCATTCAATTT
Found at i:53499 original size:5 final size:5
Alignment explanation
Indices: 53489--53606 Score: 177
Period size: 5 Copynumber: 23.0 Consensus size: 5
53479 TAGTTTACCC
53489 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
53539 TATAT TATAT ATATAT TATAT TATAT TATA- TAT-T ATATTAT TATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT -TA-TAT TATAT
53585 TATATT ATATAT TATAT TATAT
1 TATA-T -TATAT TATAT TATAT
53607 GTTGTGCAAG
Statistics
Matches: 106, Mismatches: 0, Indels: 14
0.88 0.00 0.12
Matches are distributed among these distances:
4 3 0.03
5 88 0.83
6 10 0.09
7 5 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:59770 original size:31 final size:30
Alignment explanation
Indices: 59739--59794 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
59729 CATAATATTA
*
59739 TATTAAAA-TATTAAAAAAATAAAAATAAT
1 TATTAAAATTATTAAAAAAACAAAAATAAT
*
59768 TATTAAAATTATTTAAAAAACAAAAAT
1 TATTAAAATTATTAAAAAAACAAAAAT
59795 TTGAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (30 bp):
TATTAAAATTATTAAAAAAACAAAAATAAT
Found at i:60915 original size:22 final size:22
Alignment explanation
Indices: 60890--60951 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
60880 GTGAAATTTT
*
60890 TCCCGAACGATCTATGTAGATG
1 TCCCGAAGGATCTATGTAGATG
* * **
60912 TCCCGAAGGTTCTCTGTATTTG
1 TCCCGAAGGATCTATGTAGATG
*
60934 TCCCGAAGGACCTATGTA
1 TCCCGAAGGATCTATGTA
60952 ACCCTCGACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (22 bp):
TCCCGAAGGATCTATGTAGATG
Found at i:65967 original size:22 final size:22
Alignment explanation
Indices: 65901--65967 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
65891 GGCATGTGAA
* * *
65901 ATTTGTCTCGAATGACCTATAT
1 ATTTGTCCCGAAGGACCTATGT
* * *
65923 ATATATCCCGAAGGACCTCTGT
1 ATTTGTCCCGAAGGACCTATGT
65945 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
65967 A
1 A
65968 ACCCTCGACT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:67767 original size:16 final size:16
Alignment explanation
Indices: 67746--67780 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
67736 TTACTCTACT
67746 TGTTATGAACCTGACC
1 TGTTATGAACCTGACC
67762 TGTTATGAACCTGACC
1 TGTTATGAACCTGACC
67778 TGT
1 TGT
67781 AAATGATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (16 bp):
TGTTATGAACCTGACC
Found at i:68354 original size:20 final size:20
Alignment explanation
Indices: 68187--68347 Score: 205
Period size: 20 Copynumber: 8.0 Consensus size: 20
68177 AAATTCGCGT
68187 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
* * ** *
68207 CGCAAATTTGGAAAATCGCAA
1 TGCGAA-TACGTAAATCGCAA
* *
68228 TGCGATTACGTAAATCGTAA
1 TGCGAATACGTAAATCGCAA
68248 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
68268 TGTGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
* *
68288 TGCGAATACATAAATTGCAA
1 TGCGAATACGTAAATCGCAA
*
68308 TACGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
68328 TGCGAATATGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
68348 CGTGAATCTG
Statistics
Matches: 117, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
20 103 0.88
21 14 0.12
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (20 bp):
TGCGAATACGTAAATCGCAA
Found at i:68579 original size:22 final size:22
Alignment explanation
Indices: 68553--68617 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
68543 GCGACATCCG
*
68553 TCCCCATCTCCGACAAAATCAA
1 TCCCCATCTCCGACGAAATCAA
* *
68575 TCCCCATCTCCGACGATATCAG
1 TCCCCATCTCCGACGAAATCAA
* *
68597 TCTCCATCTCCGGCGAAATCA
1 TCCCCATCTCCGACGAAATCA
68618 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.28, C:0.40, G:0.11, T:0.22
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAA
Found at i:68993 original size:20 final size:20
Alignment explanation
Indices: 68968--69020 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
68958 CGATTTTCAT
68968 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
68988 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
69008 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
69021 TTTTATTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:69028 original size:20 final size:20
Alignment explanation
Indices: 69005--69043 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
68995 TGCGATAGTC
69005 ATTTTCGTGTTGCGATTTTT
1 ATTTTCGTGTTGCGATTTTT
69025 ATTTTCGTGTTGCGATTTT
1 ATTTTCGTGTTGCGATTTT
69044 AAGTTTCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (20 bp):
ATTTTCGTGTTGCGATTTTT
Found at i:69050 original size:20 final size:20
Alignment explanation
Indices: 69007--69050 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
68997 CGATAGTCAT
* *
69007 TTTCGTGTTGCGATTTTTAT
1 TTTCGTGTTGCGATTTTAAG
69027 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
69047 TTTC
1 TTTC
69051 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:70930 original size:20 final size:20
Alignment explanation
Indices: 70905--71088 Score: 126
Period size: 20 Copynumber: 9.8 Consensus size: 20
70895 AGAATAGTTT
* *
70905 ACTATCGCAATGTGAAAATG
1 ACTATCGCAACGCGAAAATG
70925 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* *
70945 ACTATCACAA--CG-AGA-G
1 ACTATCGCAACGCGAAAATG
*
70961 A--ATCGCAATGCG-AAATG
1 ACTATCGCAACGCGAAAATG
** *
70978 AAAATCTCAA--C-AACAA--
1 ACTATCGCAACGCGAA-AATG
70994 A--ATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* *
71012 ACTATCGCAATGCGAAAACG
1 ACTATCGCAACGCGAAAATG
*
71032 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* **
71052 ACTATCGCAATGCGAATTTG
1 ACTATCGCAACGCGAAAATG
*
71072 ACTATCGCAATGCGAAA
1 ACTATCGCAACGCGAAA
71089 TGAAAATCGC
Statistics
Matches: 136, Mismatches: 14, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
14 12 0.09
16 10 0.07
17 8 0.06
18 5 0.04
19 6 0.04
20 95 0.70
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:71050 original size:40 final size:40
Alignment explanation
Indices: 70995--71105 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
70985 CAACAACAAA
*
70995 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAACGACT
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAACGACT
***
71035 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAACGACT
** *
71075 ATCGCAATGCG-AAATGAAAATCGCATTGCGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCGA
71106 TTCTCTCGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 17 0.27
40 47 0.73
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (40 bp):
ATCGCAATGCGAAAATGACTATCGCAATGCGAAAACGACT
Found at i:71200 original size:20 final size:20
Alignment explanation
Indices: 71114--71185 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
71104 GATTCTCTCG
71114 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
71134 TTGCGATAGTAAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
71154 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCAAATTCGCA
71174 TTGCGATAGTCA
1 TTGCGATAGTCA
71186 TTTTCGTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:71775 original size:21 final size:21
Alignment explanation
Indices: 71684--71788 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
71674 GACTCACCTG
*
71684 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
71706 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
71726 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
71747 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
71768 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
71789 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:71781 original size:42 final size:42
Alignment explanation
Indices: 71681--71791 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
71671 CCCGACTCAC
* * * *
71681 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
71723 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
71765 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
71792 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:73183 original size:14 final size:14
Alignment explanation
Indices: 73164--73199 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
73154 ATTGTTTAAT
73164 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
73178 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
73192 TGATTTGT
1 TGATTTGT
73200 TTAATGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:73356 original size:31 final size:33
Alignment explanation
Indices: 73302--73375 Score: 116
Period size: 31 Copynumber: 2.3 Consensus size: 33
73292 GCAAAAGTCG
73302 CGTTGCGATTTTCATTTTCGCATTGCGATTC-AT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTAT
*
73335 CGTTGCGATTTTCA-TTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
73367 CGTTGCGAT
1 CGTTGCGAT
73376 AGTTATTTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 15 0.38
32 10 0.26
33 14 0.36
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
Found at i:73390 original size:18 final size:18
Alignment explanation
Indices: 73367--73425 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
73357 GCGATTCTCT
*
73367 CGTTGCGATAGTTATTTC
1 CGTTGCGATAGTAATTTC
*
73385 CGTTGCGATAGTCAATTCC
1 CGTTGCGATAGT-AATTTC
*
73404 GCGTTGCGATAGTCATTTC
1 -CGTTGCGATAGTAATTTC
73423 CGT
1 CGT
73426 GTTGCAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 15 0.43
19 8 0.23
20 12 0.34
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (18 bp):
CGTTGCGATAGTAATTTC
Found at i:73422 original size:38 final size:40
Alignment explanation
Indices: 73367--73443 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
73357 GCGATTCTCT
* *
73367 CGTTGCGATAGTTATTTCC-GTTGCGATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCCGGTTGCAATAGTCATATTCCG
73405 CGTTGCGATAGTCATTTCCGTGTTGCAATAGTCATATTC
1 CGTTGCGATAGTCATTTCCG-GTTGCAATAGTCATATTC
73444 GTGTTACGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 18 0.53
40 12 0.35
41 4 0.12
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGGTTGCAATAGTCATATTCCG
Found at i:73446 original size:20 final size:21
Alignment explanation
Indices: 73368--73453 Score: 94
Period size: 20 Copynumber: 4.4 Consensus size: 21
73358 CGATTCTCTC
*
73368 GTTGCGATAGTTAT-TTCC--
1 GTTGCGATAGTCATATTCCGT
*
73386 GTTGCGATAGTCA-ATTCCGC
1 GTTGCGATAGTCATATTCCGT
73406 GTTGCGATAGTCAT-TTCCGT
1 GTTGCGATAGTCATATTCCGT
*
73426 GTTGCAATAGTCATATT-CGT
1 GTTGCGATAGTCATATTCCGT
*
73446 GTTACGAT
1 GTTGCGAT
73454 TTCCGCGTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
18 16 0.28
20 40 0.69
21 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (21 bp):
GTTGCGATAGTCATATTCCGT
Done.